Troubleshooting

Chrome Extension

The Chrome extension is required
to run Paperpile. Installation and update of the Chrome
extension is fast and simple and requires minimal interaction
on your part. Here are some tips when you run into
problems. More general information on how to manage extensions
can be found here.

Installing the Chrome extension

Paperpile will ask you to install the extension the first
time you use Paperpile on a computer. Click "Install
extension" and the extension will be downloaded and
installed automatically.

In some rare cases, the download or
install may fail with an error message. Try the following:

If it still won't work, try signing out and back
in to your Google Account. Click here to sign out.

Required Chrome version

Paperpile currently requires Chrome or Chromium version 27
or higher. The Chrome browser usually auto-updates regularly,
so no maintenance is required to ensure you have the latest
version. However, some systems (especially Linux-based systems
using the Chromium variant) may be out-of-date. If this is the
case and the Paperpile extension cannot be installed, try
updating your Chrome / Chromium installation.

Enable/Disable/Restart the Chrome extension

You should make sure that the Paperpile Chrome extension is always enabled. To verify this, go
to Tools > Extensions in the Chrome
menu . In the extensions tab, find Paperpile in
the list and check that it is "Enabled".

If Paperpile shows a message "Lost contact with Chrome extension"
or Paperpile is behaving strangely in some other way,
reloading the extension might help. Go to the extension tab
and disable and then re-enable the extension. Alternatively,
restart Chrome, which will restart all extensions.

Updating the Chrome extension

Chrome will automatically update your extension in the
background. Sometimes if Chrome has not updated the
extension yet, you will see an update window in
Paperpile. Similar to the install process described above,
click "Update Extension" to automatically download
and update the extension. If the update fails, you can
manually update the extension by going to Tools >
Extensions in the Chrome
menu . In the extension tab, activate "Developer
mode" and click "Update extensions now".

File Uploads

When you upload a file, Paperpile stores a temporary copy of
the file within your browser while scanning it and importing
references. PDFs are then permanently stored within your
browser's controlled storage for easy access.

This
file access requires certain access permissions from Chrome;
you may have trouble uploading files if you configured Chrome
with heightened security or privacy settings. Here are some
tips on what to do.

Filesystem Access

Certain Chrome privacy settings may cause Paperpile to be
denied access to Chrome's internal filesystem, which is
needed to store temporary files during uploads. There are
two ways to resolve this issue, depending on your privacy
needs.

Option 1 (Preferred): Allow third-party cookies and site data

Open Chrome's settings tab by clicking the
Chrome menu and choosing Settings

Toward the bottom of the page, click ,
then click
to open the content settings dialog.

Make sure that "Allow local data to be set" is selected
and "Block third-party cookies and site data" is
not checked (example).

Refresh Paperpile and start uploading your files.

Option 2: Add security exceptions for Paperpile

If you prefer to continue blocking other third-party
cookies and site data, you can add two exceptions to your
Content Settings that will specifically allow Paperpile to access the
filesystem as normal.

Supported Filetypes

If you try to import a file with a filetype not supported
by Paperpile, it will not be included in the upload. A
warning will be shown whenever an unsupported file is
encountered.

Paperpile can import references from the following file
types:

BibTeX (.bib)

RIS (.ris or .txt)

PDF (.pdf)

If you are trying to upload a BibTeX or RIS file that
does not have a file extension, please rename the file with an appropriate
extension to allow it to be recognized (e.g. rename "MyLibrary" to
"MyLibrary.ris").

Note: although Paperpile only supports certain
filetypes for import, you can attach any type
of file to a paper in your library. Click the attachments
tab, then choose "Attach supplementary PDF or other files"
and browse for the file to attach.

Google Docs Plug-in

Paperpile uses a service called
Google Apps Script to format citations within your
documents. Most problems with Apps Script are easily resolved,
but like any cloud-based service, Apps Script can suffer
occasional outages. Here are some tips for what to do when
something has gone wrong.

Installation

The Google Docs plug-in requires no special installation
— if you have installed the Chrome extension and are
logged into Paperpile, the plug-in will load automatically
when you open a Google Doc. To verify this, look for the
"Paperpile" menu and the "P" button on the right of the
toolbar.

If the plug-in is not loading: make sure you are
logged into Paperpile by visiting paperpile.com, then reload
the Google Docs tab. If the plug-in is still not loading, try
reloading the Chrome extension (instructions are here).

If you wish to disable the Docs plug-in at any point, you
can access this setting from the Paperpile settings panel:
Settings > Browser
Integration.

Authorization

The first time you format a Google Document, the Paperpile
plug-in must be authorized. This allows the Paperpile plug-in
to scan and modify your document with the same permissions as
you do. Note that Paperpile will only process your document
when explicitly triggered to do so.

When you click "Authorize plug-in", a window will pop up
indicating that the script requires authorization.

Click Continue and a second
window will show, listing the permissions to be granted to the
Paperpile plug-in:

Click Accept and the windows
should close automatically, allowing you to continue
formatting your document.

In rare cases, an issue with the Apps Script service has
caused this authentication to fail, yielding a message "The
script has been denied access to your data." even when a user
clicks Accept:

This authorization error is usually temporary, possibly
caused by an outage in the Apps Script system. Please try
again in an hour, or contact support if the issue
persists.

Google Accounts

The Google Docs plugin can only be run when using Google
Docs with your Paperpile-linked Google Account. Look at the
upper-right corner of both the Paperpile and Google Docs
browser tabs. If the email address shown in each tab is the
same, then the Paperpile plug-in should work correctly.

Your email should be the same in Paperpile (left) and Google Docs (right)

Multiple accounts: The Paperpile plugin might not
work correctly if you are using Google Docs (or other Google
services) simultaneously with multiple Google accounts across
different tabs. In that case, sign out completely from all
Google Docs tabs and sign-in again only with your
Paperpile-linked Google account.

Shared documents: Sometimes it can take up to 15
minutes for changes in the sharing status of a document to
propagate to the Paperpile Docs plug-in. If a document was
recently shared with you and you are seeing an "authorization"
error when formatting citations, wait a while and try again
before contacting support.

Formatting Problems

If an error occurs when formatting your document, Paperpile
will display a list of messages indicating what went
wrong. Here is a summary of known errors and potential
solutions:

The Paperpile server took too long to respond.

The Paperpile server takes your citation data and turns
it into foramtted textual citations and a biliography,
which usually takes just a few seconds. This message is
shown when that network request takes longer than 30
seconds or fails entirely. The entire Paperpile server may
be down or experiencing heavy load, or a temporary network
glitch may cause the issue.

Since Google Docs allows real-time collaboration, a
document being written by several coauthors may be
changing rapidly. If citations are added or removed
while you are formatting a document, the plug-in
may detect an inconsistent state and fail to continue.

Try formatting your document again once the active
editing of citations has slowed.

There was an error styling the text for one of your citations.

In rare circumstances, Paperpile will fail to correctly
set the style (e.g., italics, bold) for an inline
citation. This may happen when a citation is at the very
end of a paragraph.

Try re-formatting your document; often these isolated
errors go away after re-running the processor. If the
problem persists, try adding or removing some text before
or after the problematic citation and re-format
again.

An error occurred when loading one or more of your citations.

If something makes it impossible for Paperpile to find
your citations in its database (e.g. a broken identifier
in your document, or an unexpected database failure) you
may see this message, along with the text "[Citation
error]" somewhere in your document.

The best solution here is to remove the "[Citation
error]" text, re-insert the original citation, and
re-format your document.

An unexpected / Google Apps Script error occurred

The actual modification of your document is done via
Google Apps Script, a programming environment for Google
Docs. Since Apps Script is an evolving product, unexpected
issues may arise that were not accounted for by the
Paperpile developers. If you see this message, they have
already been notified of this error and may get in touch
with you for more details.

You can try reformatting your document to see if the
error is not repeated.

Library Import

Paperpile supports one-click import of your library from your
Mendeley or Zotero library if it has been synced to the
web. This feature has been tested to work with large and
complex libraries, but unexpected errors may sometimes
occur.

If the library import fails, you may see one of the
following error messages:

Too many duplicates were encountered during import

This message will occur if you attempt to import a web
library with many papers that are identical to items already
in your library. Most likely, your web library has already
been imported, in which case you should delete your existing
imported folder before re-trying the import. (Note:
Paperpile does not sync papers with Mendeley or
Zotero — library import should only be run once!)

An unexpected error occurred

This message may be shown if the Zotero or Mendeley web
service is unavailable, or if an unrecoverable error
occurred while downloading data from their external
servers. Wait a few minutes before trying again, and if the
error persists please contact Paperpile support.

Opening File Attachments

When you click to view a PDF in Paperpile, the actual file may
be located on your computer, synced to your Google Drive
account, or on another user's Google Drive space.

Occasionally, you may run into trouble when attempting to open
a PDF file from your computer or online. Below are some of the
most common causes and solutions for errors opening
attachments.

PDF downloaded from a different computer and not synced to Google Drive

When Paperpile first downloads a PDF it is stored on your
computer's hard drive. In most cases, the file is then
automatically synced to Google Drive, at which point it
becomes accessible from any of your other machines. If
you share this paper with collaborators, they can only
access the PDF once it has synced to Google Drive.

Very occasionally the Drive sync process won't
complete. This may be due to a network problems or browser
shutdown, and will leave some files unsynced. If you then
attempt to open these files from another computer, you may
see an error message:

Solution: Usually the easiest solution is to
return to the computer from which you downloaded the files
and start a new sync to Google Drive. Click the Drive icon
in the upper-right part of the screen and select "Start Sync
Now". The sync should begin running and complete within a
few minutes.

The file is larger than 20 MB.
Currently Paperpile only syncs files smaller than 20 MB. All
other files are only stored locally on the computer where
you imported it. We will add syncing of files of arbitrary
size in the future.

If the problematic file(s) won't load from any of your
machines: There is a chance that the browser-based
filesystem where Paperpile initially stores PDFs was cleared
or ran out of disk space. Check your machine for low disk
space, ensure that no other software is affecting Chrome's
built-in storage space, and contact Paperpile Support if you
need further assistance.

If a file cannot be recovered: As a last resort,
you can remove a "missing" file from your Paperpile library
in order to re-download or re-upload the article PDF. First,
click the "Paperclip" icon to view the attachment for a
given item, then click the "Remove" link beneath the
filename. This will remove the attachment from Paperpile's
database, after which point you can re-insert the
appropriate file. After the replacement file is inserted,
make sure the Google Drive sync completes successfully to
ensure your data won't be lost in the future!

Shared file(s) unavailable from Google Drive: in
some cases, a file may be correctly synced to Google Drive
but unavailable to you for other reasons. In this case you
may see a message like those above, or a slightly different
notice:

A variety of problems may cause a synced file to fail to
download. Someone who shared papers with you may have
inadvertently deleted those PDFs while cleaning their cloud
storage, or Google Drive may be experiencing a temporary
outage. You can check
Google's service status and verify that your Internet
connection is working. If the problem persists, contact the
owner of the Paperpile item you are trying to open or get in
touch with Paperpile Support.

PDF Downloads

Paperpile supports automatically downloading PDFs from an
extensive number of journal and publisher websites. However,
some smaller journals are not yet supported, and full-text
paywalls may be encountered at subscription-based journal
websites. Here are some tips on troubleshooting PDF downloads.

If Paperpile fails to download a PDF, you will see one of
the following messages in the main item display:

PDF not found

This message is shown when Paperpile attempted to
auto-download a PDF file but failed to locate the
PDF. Paperpile may not yet support automatic PDF downloads
from this journal or publisher, or there may be an error in
the way Paperpile locates PDFs for this journal. Click
Report in the pop-up panel to notify Paperpile
Support.

PDF restricted

This message is shown when Paperpile detects that a
paywall has been encountered while attempting to
automatically download a PDF. This may happen while you are
using Paperpile off-campus or if your institute does not
subscribe to the given journal.

If you think the paywall message is in error, try
visiting the journal's website using the blue link. If you can access the full-text
PDF without trouble, use the Report link in the
pop-up panel (example) to notify Paperpile Support.

No PDF links found

This message is shown when Paperpile could not find a
supported PDF link within the set of links contained in the
paper. Check to ensure that a link to the publisher's
website exists (this can be done by opening the Edit window
for the given paper). If no such publisher's link exists,
try running Auto-Update to automatically fetch more
complete metadata from online.

If a link to the publisher's website does exist,
then Paperpile may not yet support PDF downloads for the
given publisher. Click Report to contact Paperpile
Support — we are always working to improve our PDF
download coverage, and sending a report will signal to us
that users would benefit from expanding coverage to this
publisher.

Proxy connection failed

This message is shown when you have configured
a proxy server for remote access but
Paperpile could not connect to the server. The most common
reason is you are not logged in to your institution's or
library's proxy. Follow the link to log in and retry.

Other options for adding PDFs

If the automatic PDF download fails, Paperpile provides
several options for adding a PDF to an item in your
library. Click the "Add PDF" menu to see the options:

Browse Manually: This option will open a new tab
at the paper's main website. If you can manually identify
the fulltext PDF in this website, right-click on the PDF
link and choose Paperpile > Attach
File to... to attach the PDF to this paper.

Search Google: This option will open a new tab
with a PDF-specific Google search for the current article
title. Often, authors will post a reprint of an article on
their institutional website. If you find a suitable PDF in
the search results, click Select PDF to download and
attach the PDF to your library item.

Choose a File...: This option will open a file
upload dialog, allowing you to chose a PDF file from your
computer to attach to the current item in your library.

Search within PDFs

Paperpile's default PDF view provides a note-taking
panel and toolbar that allows you to share, export,
or download the current paper:

Unfortunately, when Chrome's built in PDF viewer is
"wrapped" inside a web-page in this way, Chrome does not
allow you to search within the PDF using Ctrl-F. If you want
to search within the PDF there are two things you can do:

View plain PDFs by default: You can change your
PDF viewing preference by visiting the Paperpile settings
panel at Settings > Browser
Integration. Changing to the "Default PDF viewer"
will set Paperpile to open PDFs in a plain tab.

Vote for the Chrome bug to be fixed: this bug has
been in Chrome for a long time, but it has not yet been
fixed. You can visit the page for Chrome Issue 170478 and click the star
icon to cast your vote for this bug to be fixed.

Server Communication

The web application and Chrome extension communicate with
Paperpile's servers in order to read, write and update items
in your library. Communication with the server can fail for a
number of reasons:

You are logged out of Paperpile. If you are
starting Paperpile from a new computer or if you haven't
logged in for a long time, you may have been logged out of
Paperpile. Just visit Paperpile to sign in
again. Once you have signed in, try reloading your desired
page or re-running your desired action.

Your network connection has been lost. Paperpile
currently requires an Internet connection to operate
normally, so a slow or missing network link will disable
most important operations.

Sharing Papers with Colleagues

Paperpile comes with powerful
features for privately sharing papers and PDFs with your
colleagues. Visit the sharing
guide to learn more about how sharing with Paperpile
works; here are some tips for what to do when you encounter
common sharing issues.

A shared folder could not be found

This message may occur if a colleague added you to the
folder using an email address other than the one associated
with your Paperpile account. Contact your colleague and
request that they add you to the folder using your Paperpile
email address; once this is done, the shared folder will show
up the next time you open Paperpile.

Alternatively, the shared folder may have been
deleted by the owner and is not available anymore.

Problems with shared web links

You can share papers via unique web links. Anyone with the
link can access the list of papers and associated PDFs and
supplementary files. Some issues you may encounter accessing
shared links and downloading shared files:

Paper collection could not be found. The link you
are trying to view may not be correct. Make sure you use the
exact and complete link that was shared with
you. Alternatively, if you are trying to view a shared
folder through a web link, the owner might have deleted the
folder and it is not available anymore. Ask the user who has
shared the link with you for a correct and up-to date
link.

File download expired. Paperpile's sharing
feature is intended for personal sharing of references and
files between collaborators, not for public distribution
of articles. In order to mitigate large-scale downloads,
Paperpile limits the number of times a PDF may be
downloaded via the web. Please ask the folder's owner to
re-share the disabled item if you have a legitimate need
to access the privately-shared content.

File download error. File downloads only work if
the owner of the file has synced the file to his or her
Google Drive. If a download fails it might be a temporary
problem with Google Drive servers. Try again after a few
minutes. If the error persists ask the owner of the file
to sign-in to Paperpile and double check that the file is
synced to Google Drive and syncing is activated. More
information how to activate syncing and check the syncing
state of a file is available in
our syncing guide.

Contacting Support

If you are experiencing an issue
not covered by this troubleshooting guide, or if you think you
found a bug, don't hesitate to contact us!

You can
send us a message from within Paperpile by clicking the "?"
button in the lower-right corner of the screen, or email us at
support@paperpile.com.

Copying your Paperpile debug information

Our support team may ask you to share with us some debug
information recorded by the Paperpile Chrome
extension. Follow these steps to locate this info: